ORIGINAL ARTICLE A combined morphometric and AFLP based diversity study challenges the taxonomy of the European members of the complex Prunus L. section Prunus Leander Depypere Æ Peter Chaerle Æ Peter Breyne Æ Kristine Vander Mijnsbrugge Æ Paul Goetghebeur Received: 24 October 2008 / Accepted: 25 January 2009 / Published online: 17 March 2009 Ó Springer-Verlag 2009 Abstract Multivariate analysis of both endocarp and leaf morphometrics is combined with cluster analysis and Bayesian inference of AFLP markers to assess the mor- phologic and genetic variation of five European members of Prunus section Prunus (P. cerasifera, P. domestica, P. insititia, P. spinosa, and P. 9 fruticans). Endocarp morphometrics separate most Prunus taxa studied, but overlap remains between P. domestica and P. cerasifera, and P. spinosa and P. 9 fruticans. Leaf morphometrics yield better separation of P. domestica and P. cerasifera, but do not allow distinction between P. spinosa and P. 9 fruticans. Both cluster analysis and PCoA of AFLP markers equally produce three distinct clusters. A first consists of all P. cerasifera samples and the sole P. co- comilia; a second cluster includes all individuals of P. domestica and P. insititia; and a third group comprises all P. spinosa and P. 9 fruticans samples. Keywords Prunus L. section Prunus Á Eurasian plums Á Morphometrics Á AFLP Á Phenetic analysis Á Taxonomy Introduction The genus Prunus L. (Rosaceae) is naturally distributed in the temperate regions of the Northern Hemisphere with some species occurring in the tropical and subtropical regions (Rehder 1940; Kru ¨ssmann 1978; Scholz and Scholz 1995; Kalkman 2004; Mabberley 2008). The genus com- prises around 200 species and is traditionally divided into five subgenera: Amygdalus (L.) Focke, Cerasus Pers., Laurocerasus Koehne, Padus (Moench) Koehne, and Prunus (Rehder, 1940). The subgenus Prunus, consists of three sections: Armeniaca (Lam.) Koch. (Apricots), Pru- nocerasus Koehne (North American plums), and Prunus (Eurasian plums) (Rehder, 1940). Following Mason (1913) and Rehder (1940), the section Prunus consists of P. cerasifera Ehrh. (Cherry plum or Myrobalan plum), P. divaricata Ledeb. [=Prunus cerasifera Ehrh. var. divaricata (Ledeb.) L. H. Bailey], P. domestica L. (Euro- pean plum), P. salicina Lindl. (Japanese plum), P. simonii Carr. (Apricot plum), and P. spinosa L. (Hawthorn or Sloe). Based on sequence analysis of ITS and trnL–trnF Spacer DNA, Bortiri et al. (2001) partitioned the section Prunus in two clades: one consisting of P. salicina and P. simonii and one including P. cerasifera, P. domestica, and P. spinosa. This division is consistent with results from isozyme data (Mowrey and Werner 1990) and cpDNA sequence analysis (Shaw and Small, 2004). The close relationship between P. cerasifera, P. domestica (including P. insititia), and P. spinosa has been demonstrated by a number of morphologic studies (Hanelt 1997; Ku ¨hn 1999; Woldring 2000; Nielsen and Olrik 2001) and has been confirmed in several genetic analyses (Bortiri et al. 2001; Aradhya et al. 2004; Shaw and Small 2004; Katayama and Uematsu 2005). Still, taxonomic delineation of these taxa is problematic, and their mutual relationships are far from well resolved. Several factors may have contributed to the complexity of this polymorphic group. Most probably, polyploidisation events (e.g., Reynders and Salesses 1991; Zohary 1992; Scholz and Scholz 1995; Ko ¨rber-Grohne L. Depypere (&) Á P. Chaerle Á P. Goetghebeur Research Group Spermatophytes, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium e-mail: Leander.Depypere@UGent.be P. Breyne Á K. Vander Mijnsbrugge Research Institute for Nature and Forest, Scientific Institute of the Flemish Government, Gaverstraat 4, 9500 Geraardsbergen, Belgium 123 Plant Syst Evol (2009) 279:219–231 DOI 10.1007/s00606-009-0158-8